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Predictions of the secondary structure of T4 phage lysozyme, made by a number of
investigators on the basis of the amino acid sequence, are compared with the
structure of the protein determined experimentally by X-ray crystallography.
Within the amino terminal half of the molecule the locations of helices
predicted by a number of methods agree moderately well with the observed
structure, however within the carboxyl half of the molecule the overall
agreement is poor. For eleven different helix predictions, the coefficients
giving the correlation between prediction and observation range from 0.14 to
0.42. The accuracy of the predictions for both beta-sheet regions and for turns
are generally lower than for the helices, and in a number of instances the
agreement between prediction and observation is no better than would be expected
for a random selection of residues. The structural predictions for T4 phage
lysozyme are much less successful than was the case for adenylate kinase (Schulz
et al. (1974) Nature 250, 140-142). No one method of prediction is clearly
superior to all others, and although empirical predictions based on larger
numbers of known protein structure tend to be more accurate than those based on
a limited sample, the improvement in accuracy is not dramatic, suggesting that
the accuracy of current empirical predictive methods will not be substantially
increased simply by the inclusion of more data from additional protein structure
determinations.
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